Non-specific backbone staining of nucleic acids with intercalating dyes is a fundamental requirement of certain nucleic acid manipulations and analyses. (Chan, Goncalves et al. 2004; Jung, Bharadwaj et al. 2006; Larson, Yantz et al. 2006; Shackman and Ross 2007; Protozanova, Zhang et al. 2010). As an example, in Direct Linear Analysis (DLA) or Genome Sequence Scanning (GSS™), backbone specific staining is used to determine presence, velocity and length of nucleic acids.
Typically, intercalation reactions are performed by adding an appropriate mass of a specific intercalating dye to a known mass of DNA, resulting in a fixed molar ratio of individual fluorophores to nucleic acid base pairs. However, variable starting cell load, genomic content, and DNA extraction efficiencies can cause the mass yields between sample preparations to be inconsistent. This can complicate analyses by requiring that nucleic acid mass be pre-quantified.